MetNetComp Database [1] / Minimal gene deletions

Minimal gene deletions for simulation-based growth-coupled production. You can also see maximal gene deletions.

Model : iML1515 [2].
Target metabolite : prlp_c
List of minimal gene deletion strategies (Download)

Gene deletion strategy (59 of 71: See next) for growth-coupled production (at least stoichioemetrically feasible)
  Gene deletion size : 36
  Gene deletion: b2836 b4382 b4384 b3708 b3008 b0871 b2779 b2925 b2097 b0030 b2407 b2690 b1982 b2797 b3117 b1814 b4471 b0261 b3945 b0507 b2406 b0112 b0114 b0886 b0529 b1539 b2492 b0904 b2578 b1533 b3927 b1380 b0594 b0515 b3662 b1813   (List of alternative genes)
  Computed by: RandTrimGdel [1] (Step 1, Step 2)

When growth rate is maximized,
  Growth Rate : 0.573478 (mmol/gDw/h)
  Minimum Production Rate : 0.129990 (mmol/gDw/h)

 Substrate: (mmol/gDw/h)
  EX_o2_e : 27.111174
  EX_glc__D_e : 10.000000
  EX_nh4_e : 6.852416
  EX_pi_e : 0.813160
  EX_so4_e : 0.144413
  EX_k_e : 0.111939
  EX_fe2_e : 0.009211
  EX_mg2_e : 0.004975
  EX_cl_e : 0.002985
  EX_ca2_e : 0.002985
  EX_cu2_e : 0.000407
  EX_mn2_e : 0.000396
  EX_zn2_e : 0.000196
  EX_ni2_e : 0.000185
  EX_cobalt2_e : 0.000014

Product: (mmol/gDw/h)
  EX_h2o_e : 46.154736
  EX_co2_e : 26.711197
  EX_h_e : 8.519089
  EX_pyr_e : 2.589244
  Auxiliary production reaction : 0.129990
  EX_alltn_e : 0.002239
  DM_5drib_c : 0.001982
  DM_4crsol_c : 0.001725
  EX_glyclt_e : 0.001597

Visualization
  1. Download JSON file.
  2. Go to Escher site [3].
  3. Select "Data > Load reaction data" and apply the downloaded file.

References
[1] Tamura, T. MetNetComp: Database for minimal and maximal gene deletion strategies for growth-coupled production of genome-scale metabolic networks, IEEE/ACM Transactions on Computational Biology and Bioinformatics, in press.
[2] Norsigian, C. J., Pusarla, N., McConn, J. L., Yurkovich, J. T., Dräger, A., Palsson, B. O., & King, Z. (2020). BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree. Nucleic acids research, 48(D1), D402-D406.
[3] King, Z. A., Dräger, A., Ebrahim, A., Sonnenschein, N., Lewis, N. E., & Palsson, B. O. (2015). Escher: a web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS computational biology, 11(8), e1004321.

Last updated: 21-Sep-2023
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